uchime说明书.doc

USEARCH command line ?A typical USEARCH command line looks like this: usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta | | | | | Command Input file Output file Binary filename The command line starts with the binary filename. In this manual, examples are always shown using usearch as the filename. You should use the actual name of your binary file. You can rename your binary file to usearch or use the original name, e.g. usearch6.0.98_i86linux32. The binary file must be in a directory in your shells PATH variable, otherwise you must type the full path name, e.g. (Linux or OSX): /usr/bin/usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta Under Windows, use backslashes and drive letters as needed: C:\binaries\usearch.exe -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta If the binary is in your current directory, you can use ./ or .\ (dot-slash or dot-backslash) as the path name: ./usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta Command-line optionsOptions are given after a hyphen (-). Command names are options, so must also have a hyphen. Two hyphens are allowed (Linux long option form), so both id 0.9 and --id 0.9 are allowed. There must be a space between the option name and its value, so -id0.9 is not allowed. CommandsA command line must have exactly one command. The command name is usually followed by the name of an input or query file in FASTA format. UCHIME algorithm ?UCHIME is an algorithm for detecting chimeric sequences. It is implemented in the uchime_ref and uchime_denovo commands. The fundamental step in UCHIME is a search for a 3-way alignment of a query sequence with two parent sequences (A and B) such that one parent is more similar to one segment of the query (Q) and the other parent is similar over another segment, as in the figure below. A score is calculated from the alignment. Higher scores indicate a stronger chimeric signal. A score c